The image above was taken during Father Paul Ponziglione's Jubilee celebration on February 27, 1889.  Father is at the right side of the altar facing east as the deacon chants the Gospel on the left. Bishop Hennessy is at far left. 

At the time of the photo the new St. Francis de Heironymo Catholic Church was not even five years old.  The structure was dedicated in May of 1884.  Father Ponziglione oversaw its completion after the death of his colleague, Father John Schoenmakers, the year before.

This was Father Paul's last significant event at his beloved St. Francis Church.  In August of 1889, he was sent, briefly, to Marquette College in Milwaukee.  From there, at age 72, he was sent to Wyoming for nearly two years to assist with the start of St. Stevens Mission, north of Lander.  After the Wyoming assignment, he turned in his saddle and spent his remaining years doing inner-city missionary work while assigned to St. Ignatius College, Chicago.  He passed away on March 28, 1900. [1]

A Modern Photo, Similar Position.
The photo below is from a similar angle but taken recently.  It is a sharper digital photo, but the colors have been muted slightly.  What has changed?

Even with muted colors, the stained glass windows stand out.   The large windows are at second-floor elevation and nearly align with the top of the main altar.  Smaller windows have been added to the top of the previous arched doorways.  When you look at the early photo, the upper windows appear to be double-hung with sliding lower panels.  This feature allowed those windows to be opened, so priests and others could attend Mass from above.  

A sharp eye will notice the top of the altar.  The three caps, above the statues were much taller when the original photo was taken.

But Back to the Windows.​
When St. Francis Catholic Church was dedicated in 1884, Nearly all of the windows were somewhat similar to the upper arched windows with metal inner-frames and clear glass.  It wasn't until 1900 that Father Boniface entered into a contract with the Kansas City Stained Glass Company to replace nearly all of the original clear glass windows with stained glass panels.

There are a couple of relics, of the original windows, on the back of the church.  The high arch windows, that illuminate the upstairs rooms still have the same clear glass, or at least glass that is similar to that originally installed.  The photo shown here is of the northwest corner of the church.  There is a matching upper window on the northeast corner.

The lower, stained glass window is the main sacristy window.  That window was added to the thick sandstone walls during construction of the Passionist Monastery in 1912.   More about that later.

Some Reference Information:
1.  For more information about Father Paul Mary Ponziglione, follow THIS LINK.
2.  For more information about the original construction of "the new" St. Francis Catholic Church, and major upgrades, Follow THIS LINK.